Genetic analyses of the putative O and K antigen gene clusters of pandemic Vibrio parahaemolyticus

Phenotypic changes and gene expression profiles of Vibrio parahaemolyticus in response to low concentrations of ampicillin

Vibrio parahaemolyticus is a leading cause of seafood-associated gastroenteritis and possesses intrinsic resistance to ampicillin. While ampicillin can trigger transcriptional responses of global genes, the behavioral and molecular changes that occur in V. parahaemolyticus when exposed to ampicillin are not fully understood. In this work, we investigated the effects of low concentrations of ampicillin on the physiology and gene expression of V. parahaemolyticus by combining phenotypic assays and RNA sequencing (RNA-seq) analysis. Our results showed that the growth of V. parahaemolyticus were notably delayed, and both motility and c-di-GMP production were significantly inhibited in the response to low concentrations of ampicillin stress. In contrast, biofilm formation by V. parahaemolyticus was enhanced by exposure to low concentrations of ampicillin. However, low concentrations of ampicillin had no effect on the cytotoxicity or adherence activity of V. parahaemolyticus. The RNA-seq data revealed that a low concentration of ampicillin significantly affected the expression levels of 676 genes, including those involved in antibiotic resistance, virulence, biofilm formation, and regulation. This work contributes to our understanding of how V. parahaemolyticus alters its behavior and gene expression in response to ampicillin exposure.

Antibacterial Activity of Phloretin Against Vibrio parahaemolyticus and Its Application in Seafood

Although phloretin is widely utilized in the food industry as an additive, its effects on foodborne pathogens remain insufficiently investigated. This study aimed to evaluate the antimicrobial properties of phloretin (PHL) against Vibrio parahaemolyticus (V. parahaemolyticus) and to elucidate the potential mechanisms of action. After PHL treatment, alterations in the cell morphology, cell microstructure, and intracellular contents of V. parahaemolyticus were assessed. Scanning electron microscopy revealed substantial damage to cell integrity, subsequent to PHL treatment. A notable reduction in intracellular components, including proteins, ATP, and DNA, was observed in samples treated with PHL. PHL was shown to inhibit the activities of ATPase, β-galactosidase, and respiratory chain dehydrogenase in V. parahaemolyticus. Furthermore, it was demonstrated to elevate the intracellular levels of reactive oxygen species and promote cell death. After being applied to sea bass, shrimp, and oysters, PHL effectively inactivated V. parahaemolyticus in these seafoods. These findings demonstrate that PHL has potential for application in seafood to control V. parahaemolyticus.

L-arabinose affects the growth, biofilm formation, motility, c-di-GMP metabolism, and global gene expression of Vibrio parahaemolyticus

The L-arabinose inducible pBAD vectors are commonly used to turn on and off the expression of specific genes in bacteria. The utilization of certain carbohydrates can influence bacterial growth, virulence factor production, and biofilm formation. Vibrio parahaemolyticus, the causative agent of seafood-associated gastroenteritis, can grow in media with L-arabinose as the sole carbon source. However, the effects of L-arabinose on V. parahaemolyticus physiology have not been investigated. In this study, we show that the growth rate, biofilm formation capacity, capsular polysaccharide production, motility, and c-di-GMP production of V. parahaemolyticus are negatively affected by L-arabinose. RNA-seq data revealed significant changes in the expression levels of 752 genes, accounting for approximately 15.6% of V. parahaemolyticus genes in the presence of L-arabinose. The affected genes included those associated with L-arabinose utilization, major virulence genes, known key biofilm-related genes, and numerous regulatory genes. In the majority of type III secretion system, two genes were upregulated in the presence of L-arabinose, whereas in those of type VI secretion system, two genes were downregulated. Ten putative c-di-GMP metabolism-associated genes were also significantly differentially expressed, which may account for the reduced c-di-GMP levels in the presence of L-arabinose. Most importantly, almost 40 putative regulators were significantly differentially expressed due to the induction by L-arabinose, indicating that the utilization of L-arabinose is strictly regulated by regulatory networks in V. parahaemolyticus. The findings increase the understanding of how L-arabinose affects the physiology of V. parahaemolyticus. Researchers should use caution when considering the use of L-arabinose inducible pBAD vectors in V. parahaemolyticus. IMPORTANCE The data in this study show that L-arabinose negatively affects the growth rate, biofilm formation, capsular polysaccharide production, motility, and c-di-GMP production of V. parahaemolyticus. The data also clarify the gene expression profiles of the bacterium in the presence of L-arabinose. Significantly differentially expressed genes in response to L-arabinose were involved in multiple cellular pathways, including L-arabinose utilization, virulence factor production, biofilm formation, motility, adaptation, and regulation. The collective findings indicate the significant impact of L-arabinose on the physiology of V. parahaemolyticus. There may be similar effects on other species of bacteria. Necessary controls should be established when pBAD vectors must be used for ectopic gene expression.

Effect of sublethal dose of chloramphenicol on biofilm formation and virulence in Vibrio parahaemolyticus

Vibrio parahaemolyticus isolates are generally very sensitive to chloramphenicol. However, it is usually necessary to transfer a plasmid carrying a chloramphenicol resistance gene into V. parahaemolyticus to investigate the function of a specific gene, and the effects of chloramphenicol on bacterial physiology have not been investigated. In this work, the effects of sublethal dose of chloramphenicol on V. parahaemolyticus were investigated by combined utilization of various phenotypic assays and RNA sequencing (RNA-seq). The results showed that the growth rate, biofilm formation capcity, c-di-GMP synthesis, motility, cytoxicity and adherence activity of V. parahaemolyticus were remarkably downregulated by the sublethal dose of chloramphenicol. The RNA-seq data revealed that the expression levels of 650 genes were significantly differentially expressed in the response to chloramphenicol stress, including antibiotic resistance genes, major virulence genes, biofilm-associated genes and putative regulatory genes. Majority of genes involved in the synthesis of polar flagellum, exopolysaccharide (EPS), mannose-sensitive haemagglutinin type IV pilus (MSHA), type III secretion systems (T3SS1 and T3SS2) and type VI secretion system 2 (T6SS2) were downregulated by the sublethal dose of chloramphenicol. Five putative c-di-GMP metabolism genes were significantly differentially expressed, which may be the reason for the decrease in intracellular c-di-GMP levels in the response of chloramphenicol stress. In addition, 23 genes encoding putative regulators were also significantly differentially expressed, suggesting that these regulators may be involved in the resistance of V. parahaemolyticus to chloramphenicol stress. This work helps us to understand how chloramphenicol effect on the physiology of V. parahaemolyticus.

Development of Kaptive databases for Vibrio parahaemolyticus O- and K-antigen genotyping

Vibrio parahaemolyticus is an important food-borne human pathogen and presents immunogenic surface polysaccharides, which can be used to distinguish problematic and disease-causing lineages. V. parahaemolyticus is divided in 16 O-serotypes (O-antigen) and 71 K-serotypes (K-antigen). Agglutination tests are still the gold standard for serotyping, but many V. parahaemolyticus isolates are not typable by agglutination. An alternative for agglutination tests is genotyping using whole-genome sequencing data, by which K- and O- genotypes have been curated and identified previously for other clinically relevant organisms with the software tool Kaptive. In this study, V. parahaemolyticus isolates were serotyped and sequenced, and all known and several novel O- and K-loci were identified. We developed Kaptive databases for all O- and K-loci after manual curation of the loci. In our study, we could genotype the O- and K-loci of 98 and 93 % of the genomes, respectively, with a Kaptive confidence score higher than 'none'. The newly developed Kaptive databases with the identified V. parahaemolyticus O- and K-loci can be used to identify the O- and K-genotypes of V. parahaemolyticus isolates from genome sequences.

Free lipid A and full-length lipopolysaccharide coexist in Vibrio parahaemolyticus ATCC33846

Lipid A plays an important role in the pathogenicity and antimicrobial resistance of Vibrio parahaemolyticus, but little is known about the structure and biosynthesis of lipid A in V. parahaemolyticus. In this study, lipid A species were either directly extracted or obtained by the acid hydrolysis of lipopolysaccharide from V. parahaemolyticus ATCC33846 cells and analyzed by thin-layer chromatography and high-performance liquid chromatography-tandem mass spectrometry. Several lipid A species in V. parahaemolyticus cells were characterized, and two of these species were not connected to polysaccharides. One free lipid A species has the similar structure as the hexa-acylated lipid A in Escherichia coli, and the other is a hepta-acylated lipid A with an additional secondary C16:0 acyl chain. Three lipid A species were isolated by the acid hydrolysis of lipopolysaccharide: the 1^st one has the similar structure as the hexa-acylated lipid A in E. coli, the 2^nd one is a hepta-acylated lipid A with an additional secondary C16:0 acyl chain and a secondary 2-OH C12:0 acyl chain, and the 3^rd one is equal to the 2^nd species with a phosphoethanolamine modification. These results are important for understanding the biosynthesis of lipid A in V. parahaemolyticus.

VPsero: Rapid Serotyping of Vibrio parahaemolyticus Using Serogroup-Specific Genes Based on Whole-Genome Sequencing Data

Vibrio parahaemolyticus has emerged as a significant enteropathogen in human and marine habitats worldwide, notably in regions where aquaculture products constitute a major nutritional source. It is a growing cause of diseases including gastroenteritis, wound infections, and septicemia. Serotyping assays use commercially available antisera to identify V. parahaemolyticus strains, but this approach is limited by high costs, complicated procedures, cross-immunoreactivity, and often subjective interpretation. By leveraging high-throughput sequencing technologies, we developed an in silico method based on comparison of gene clusters for lipopolysaccharide (LPSgc) and capsular polysaccharide (CPSgc) by firstly using the unique-gene strategy. The algorithm, VPsero, which exploits serogroup-specific genes as markers, covers 43 K and all 12 O serogroups in serotyping assays. VPsero is capable of predicting serotypes from assembled draft genomes, outputting LPSgc/CPSgc sequences, and recognizing possible novel serogroups or populations. Our tool displays high specificity and sensitivity in prediction toward V. parahaemolyticus strains, with an average sensitivity in serogroup prediction of 0.910 for O and 0.961 for K serogroups and a corresponding average specificity of 0.990 for O and 0.998 for K serogroups.

A Novel Molecular Method for Simultaneous Identification of Vibrio parahaemolyticus 57 K-Serogroups Using Probe Melting Curve Analysis

The serotyping of Vibrio parahaemolyticus, which is crucial to the surveillance and detection of outbreaks of vibriosis infection, has been widely used in many countries. In this study, we developed a molecular assay, named multiplex ligation reaction based on probe melting curve analysis (MLMA), for simultaneous identification of V. parahaemolyticus 57 K-serogroups. Based on the previous genomes of 418 strains including 39 K-serogroups and the 18 K-serogroups sequences from public databases, we obtained 57 K-serogroups specific gene sequences for designing primers and probes. The developed MLMA assay for identifying the V. parahaemolyticus 57 K-serogroups showed high reproducibility, with the intra- and inter-assay standard deviations and coefficients of variation of no more than 1°C and 1%, respectively. The limit of detection for all gene targets ranged from 0.1 to 1.0 ng/µl. We validated the MLMA assay with a double-blind test identifying 595 V. parahaemolyticus isolates using conventional serotyping methods for comparison. The results showed the kappa value between the MLMA assay and the traditional serological method was 0.936 and that there was a 96.97% consistency rate with conventional serotyping methods for all detected isolates. Additionally, five rare K-serogroups were identified using the MLMA assay, as well as 18 strains that could not be identified using the traditional serotyping method. Thus, the MLMA assay provides a rapid, robust, and promising tool for the molecular serotyping of V. parahaemolyticus K-serogroups and has the potential application to the detection of outbreaks and surveillance of V. parahaemolyticus infection.

Synergistic effects of endolysin Lysqdvp001 and ε-poly-lysine in controlling Vibrio parahaemolyticus and its biofilms

The synergistic antibacterial effects between endolysin Lysqdvp001 and ε-poly-lysine (ε-PL) against Vibrio parahaemolyticus (V. parahaemolyticus) were investigated in this study. Lysqdvp001 combined with ε-PL exhibited a strong antibacterial synergism against V. parahaemolyticus. The combinations of Lysqdvp001 (≥60 U/mL) and ε-PL (≥0.2 mg/mL) dramatically decreased cell density of the bacterial suspensions at both 25 °C and 37 °C. Surface zeta potential increment and membrane hyperpolarization of V. parahaemolyticus were observed after treatment by ε-PL and its combination with Lysqdvp001. More β-lactamase and β-galactosidase were leaked from V. parahaemolyticus with combined treatment of Lysqdvp001 and ε-PL than from the bacteria treated with single Lysqdvp001 or ε-PL. Fluorescence and transmission electron microscope revealed that Lysqdvp001 and ε-PL synergistically induced the damage and morphological destruction of V. parahaemolyticus cells. When applying in Gadus macrocephalus, Penaeus orientalis and oyster, the two antimicrobials' cocktail allowed for 3.75, 4.16 and 2.50 log₁₀CFU/g reductions of V. parahaemolyticus, respectively. Besides, Lysqdvp001 in combination with ε-PL removed approximately 44%-68% of V. parahaemolyticus biofilms on polystyrene, glass and stainless steel surfaces. These results demonstrated that Lysqdvp001 and ε-PL might be used together for controlling V. parahaemolyticus and the bacterial biofilms in food industry.

Genetic Structure, Function, and Evolution of Capsule Biosynthesis Loci in Vibrio parahaemolyticus

Capsule-forming extracellular polysaccharides are crucial for bacterial host colonization, invasion, immune evasion, and ultimately pathogenicity. Due to warming ocean waters and human encroachment of coastal ecosystems, Vibrio parahaemolyticus has emerged as a globally important foodborne enteropathogen implicated in acute gastroenteritis, wound infections, and septic shock. Conventionally, the antigenic properties of lipopolysaccharide (LPS, O antigen) and capsular polysaccharide (CPS, K antigen) have provided a basis for serotyping V. parahaemolyticus, whereas disclosure of genetic elements encoding 13 O-serogroups have allowed molecular serotyping methods to be developed. However, the genetic structure of CPS loci for 71 K-serogroups has remained unidentified, limiting progress in understanding its roles in V. parahaemolyticus pathophysiology. In this study, we identified and characterized the genetic structure and their evolutionary relationship of CPS loci of 40 K-serogroups through whole genome sequencing of 443 V. parahaemolyticus strains. We found a distinct pattern of CPS gene cluster across different K-serogroups and expanded its new 3'-border by identifying glpX as a key gene conserved across all K-serogroups. A total of 217 genes involved in CPS biosynthesis were annotated. Functional contents and genetic structure of the 40 K-serogroups were analyzed. Based on inferences from species trees and gene trees, we proposed an evolution model of the CPS gene clusters of 40 K-serogroups. Horizontal gene transfer by recombination from other Vibrio species, gene duplication is likely to play instrumental roles in the evolution of CPS in V. parahaemolyticus. This is the first time, to the best of our knowledge, that a large scale of CPS gene clusters of different K-serogroups in V. parahaemolyticus have been identified and characterized in evolutionary contexts. This work should help advance understanding on the variation of CPS in V. parahaemolyticus and provide a framework for developing diagnostically relevant serotyping methods.

Virulence, Antimicrobial Susceptibility, Molecular and Epidemiological Characteristics of a New Serotype of Vibrio parahaemolyticus From Diarrhea Patients

Vibrio parahaemolyticus is the main pathogen of food-borne diarrheal in coastal areas. Through the study of pathogen characteristics of 1870 V. parahaemolyticus, the isolation rate of O4:KUT had increased significantly since 2013. In this study, we analyzed virulence, antimicrobial susceptibility, molecular, and epidemiological characteristics of a new serotype named O4:KUT2. O4:KUT2 strains had tlh⁺tdh⁺trh^–toxRS/new^– characteristics and were prevalent during 2013–2015. The 91.5% O4:KUT2 serotype strains were resistant to ampicillin. The growth curves of O4:KUT2 strains were different with O4:K9, O4:K8, and O3:K6 serotype strains. O4:KUT2 strains belonged to ST332 where four strains had a large fragment inserted at recA. Compared the whole genomes of O4:KUT2 strains with O4:K9 strain which also belonged to ST322 isolated from acute diarrhea patients in Zhejiang province in 2012, no different alleles at 2249 loci was found. This finding implied that O4:KUT2 strains might be derived from O4:K9 strains. Clinical presentation of patients positive for V. parahaemolyticus O4:KUT2 were no significant difference with patients positive for O3:K6, although their genetic characteristics were different. The appearance and the increase of proportion of the new serotype O4:KUT2 strains was aware that we should not relax the monitoring of the pathogen spectrum of acute diarrheal patients.

Isolation, Molecular Characterization and Antibiotic Susceptibility Pattern of Vibrio parahaemolyticus from Aquatic Products in the Southern Fujian Coast, China

Vibrio parahaemolyticus is a major gastroenteritis-causing pathogen in many Asian countries. Antimicrobial resistance in V. parahaemolyticus has been recognized as a critical threat to food safety. In this study, we determined the prevalence and incidence of antimicrobial resistance in V. parahaemolyticus in the southern Fujian coast, China. A total of 62 isolates were confirmed in retail aquatic products from June to October of 2018. The serotype O3:K6 strains, the virulence genes tdh and trh, antibiotic susceptibility and molecular typing were investigated. Then plasmid profiling analysis and curing experiment were performed for multidrug-resistant strains. The results showed that the total occurrence of V. parahaemolyticus was 31% out of 200 samples. Five strains (8.1%) out of 62 isolates were identified as the V. parahaemolyticus O3:K6 pandemic clone. A large majority of isolates exhibited higher resistance to penicillin (77.4%), oxacillin (71%), ampicillin (66.1%) and vancomycin (59.7%). Seventy-one percent (44/62) of the isolates exhibited multiple antimicrobial resistance. All 62 isolates were grouped into 7 clusters by randomly amplified polymorphic DNA, and most of the isolates (80.6%) were distributed within cluster A. Plasmids were detected in approximately 75% of the isolates, and seven different profiles were observed. Seventy-six percent (25/33) of the isolates carrying the plasmids were eliminated by 0.006% SDS incubated at 42°C, a sublethal condition. The occurrence of multidrug-resistant strains could be an indication of the excessive use of antibiotics in aquaculture farming. The rational use of antimicrobial agents and the surveillance of antibiotic administration may reduce the acquisition of resistance by microorganisms in aquatic ecosystems.

Spreading of Pandemic Vibrio parahaemolyticus O3:K6 and Its Serovariants: A Re-analysis of Strains Isolated from Multiple Studies

In China, V. parahaemolyticus has been a leading cause of foodborne outbreaks and bacterial infectious diarrhea since the 1990s, and most infections have been associated with the pandemic V. parahaemolyticus O3:K6 and its serovariants. However, a comprehensive overview of the sero-prevalence and genetic diversity of the pandemic V. parahaemolyticus clone in China is lacking. To compensate for this deficiency, pandemic isolates in both clinical and environmental Chinese samples collected from multiple studies were analyzed in this study. Surprisingly, as many as 27 clinical pandemic serovariants were identified and were widely distributed across nine coastal provinces and two inland provinces (Beijing and Sichuan). O3:K6, O4:K68, and O1:KUT represented the predominant clinical serovars. Only four environmental pandemic serovariants had previously been reported, and they were spread throughout Shanghai (O1:KUT, O3:K6), Jiangsu (O3:K6, O4:K48), Zhejiang (O3:K6), and Guangdong (O4:K9). Notably, 24 pandemic serovariants were detected within a short time frame (from 2006 to 2012). The pandemic isolates were divided into 15 sequence types (STs), 10 of which fell within clonal complex (CC) 3. Only three STs (ST3, ST192, and ST305) were identified in environmental isolates. Substantial serotypic diversity was mainly observed among isolates within pandemic ST3, which comprised 21 combinations of O/K antigens. The pandemic O3:K6 serotype showed a high level of sequence diversity, which was shared by eight different STs (ST3, ST227, ST431, ST435, ST487, ST489, ST526, and ST672). Antimicrobial susceptibility testing revealed that most isolates shared similar antibiotic susceptibility profiles. They were resistant to ampicillin but sensitive to most other drugs that were tested. In conclusion, the high levels of serotypic and genetic diversity of the pandemic clone suggest that the involved regions are becoming important reservoirs for the emergence of novel pandemic strains. We underscore the need for routine monitoring to prevent pandemic V. parahaemolyticus infection, which includes monitoring antimicrobial responses to avoid excessive misuse of antibiotics. Further investigations are also needed to delineate the specific mechanisms underlying the possible seroconversion of pandemic isolates.

Sero-Prevalence and Genetic Diversity of Pandemic V. parahaemolyticus Strains Occurring at a Global Scale

Pandemic Vibrio parahaemolyticus is an emerging public health concern as it has caused numerous gastroenteritis outbreaks worldwide. Currently, the absence of a global overview of the phenotypic and molecular characteristics of pandemic strains restricts our overall understanding of these strains, especially for environmental strains. To generate a global picture of the sero-prevalence and genetic diversity of pandemic V. parahaemolyticus, pandemic isolates from worldwide collections were selected and analyzed in this study. After a thorough analysis, we found that the pandemic isolates represented 49 serotypes, which are widely distributed in 22 countries across four continents (Asia, Europe, America and Africa). All of these serotypes were detected in clinical isolates but only nine in environmental isolates. O3:K6 was the most widely disseminated serotype, followed by O3:KUT, while the others were largely restricted to certain countries. The countries with the most abundant pandemic serotypes were China (26 serotypes), India (24 serotypes), Thailand (15 serotypes) and Vietnam (10 serotypes). Based on MLST analysis, 14 sequence types (STs) were identified among the pandemic strains, nine of which fell within clonal complex (CC) 3. ST3 and ST305 were the only two STs that have been reported in environmental pandemic strains. Pandemic ST3 has caused a wide range of infections in as many as 16 countries. Substantial serotypic diversity was mainly observed among isolates within pandemic ST3, including as many as 12 combinations of O/K serotypes. At the allele level, the dtdS and pntA, two loci that perfectly conserved in CC3, displayed a degree of polymorphism in some pandemic strains. In conclusion, we provide a comprehensive understanding of sero-prevalence and genetic differentiation of clinical and environmental pandemic isolates collected from around the world. Although, further studies are needed to delineate the specific mechanisms by which the pandemic strains evolve and spread, the findings in this study are helpful when seeking countermeasures to reduce the spread of V. parahaemolyticus in endemic areas.

Genetic characterization of trh positive Vibrio spp. isolated from Norway

The thermostable direct hemolysin (TDH) and/or TDH-related hemolysin (TRH) genes are carried by most virulent Vibrio parahaemolyticus serovars. In Norway, trh+ V. parahaemolyticus constitute 4.4 and 4.5% of the total number of V. parahaemolyticus isolated from blue mussel (Mytilus edulis) and water, respectively. The trh gene is located in a region close to the gene cluster for urease production (ure). This region was characterized in V. parahaemolyticus strain TH3996 and it was found that a nickel transport operon (nik) was located between the first gene (ureR) and the rest of the ure cluster genes. The organization of the trh-ureR-nik-ure gene cluster in the Norwegian trh+ isolates was unknown. In this study, we explore the gene organization within the trh-ureR-nik-ure cluster for these isolates. PCR analyses revealed that the genes within the trh-ureR-nik-ure gene cluster of Norwegian trh+ isolates were organized in a similar fashion as reported previously for TH33996. Additionally, the phylogenetic relationship among these trh+ isolates was investigated using Multilocus Sequence Typing (MLST). Analysis by MLST or ureR-trh sequences generated two different phylogenetic trees for the same strains analyzed, suggesting that ureR-trh genes have been acquired at different times in Norwegian V. parahaemolyticus isolates. MLST results revealed that some pathogenic and non-pathogenic V. parahaemolyticus isolates in Norway appear to be highly genetically related.

Genetic relationships of Vibrio parahaemolyticus isolates from clinical, human carrier, and environmental sources in Thailand, determined by multilocus sequence analysis

Vibrio parahaemolyticus is a seafood-borne pathogenic bacterium that is a major cause of gastroenteritis worldwide. We investigated the genetic and evolutionary relationships of 101 V. parahaemolyticus isolates originating from clinical, human carrier, and various environmental and seafood production sources in Thailand using multilocus sequence analysis. The isolates were recovered from clinical samples (n = 15), healthy human carriers (n = 18), various types of fresh seafood (n = 18), frozen shrimp (n = 16), fresh-farmed shrimp tissue (n = 18), and shrimp farm water (n = 16). Phylogenetic analysis revealed a high degree of genetic diversity within the V. parahaemolyticus population, although isolates recovered from clinical samples and from farmed shrimp and water samples represented distinct clusters. The tight clustering of the clinical isolates suggests that disease-causing isolates are not a random sample of the environmental reservoir, although the source of infection remains unclear. Extensive serotypic diversity occurred among isolates representing the same sequence types and recovered from the same source at the same time. These findings suggest that the O- and K-antigen-encoding loci are subject to exceptionally high rates of recombination. There was also strong evidence of interspecies horizontal gene transfer and intragenic recombination involving the recA locus in a large proportion of isolates. As the majority of the intragenic recombinational exchanges involving recA occurred among clinical and carrier isolates, it is possible that the human intestinal tract serves as a potential reservoir of donor and recipient strains that is promoting horizontal DNA transfer, driving evolutionary change, and leading to the emergence of new, potentially pathogenic strains.

Prokaryotic systematics in the genomics era

As an essential and basic biological discipline, prokaryotic systematics is entering the era of genomics. This paradigmatic shift is significant not only for understanding molecular phylogeny at the whole genome level but also in revealing the genetic or epigenetic basis that accounts for the phenotypic criteria used to classify and identify species. These developments provide an opportunity and a challenge for systematists to reanalyze the molecular mechanisms underlying the taxonomic characteristics of prokaryotes by drawing the knowledge from studies of genomics and/or functional genomics employing platform technologies and related bioinformatics tools. It is expected that taxonomic books, such as Bergey's Manual of Systematic Bacteriology may evolve into a systematics library indexed by phylogenomic information with an comprehensive understanding of prokaryotic speciation and associated increasing knowledge of biological phenomena.

Comparative genomic analysis of Vibrio parahaemolyticus: serotype conversion and virulence

BACKGROUND

Vibrio parahaemolyticus is a common cause of foodborne disease. Beginning in 1996, a more virulent strain having serotype O3:K6 caused major outbreaks in India and other parts of the world, resulting in the emergence of a pandemic. Other serovariants of this strain emerged during its dissemination and together with the original O3:K6 were termed strains of the pandemic clone. Two genomes, one of this virulent strain and one pre-pandemic strain have been sequenced. We sequenced four additional genomes of V. parahaemolyticus in this study that were isolated from different geographical regions and time points. Comparative genomic analyses of six strains of V. parahaemolyticus isolated from Asia and Peru were performed in order to advance knowledge concerning the evolution of V. parahaemolyticus; specifically, the genetic changes contributing to serotype conversion and virulence. Two pre-pandemic strains and three pandemic strains, isolated from different geographical regions, were serotype O3:K6 and either toxin profiles (tdh+, trh-) or (tdh-, trh+). The sixth pandemic strain sequenced in this study was serotype O4:K68.

RESULTS

Genomic analyses revealed that the trh+ and tdh+ strains had different types of pathogenicity islands and mobile elements as well as major structural differences between the tdh pathogenicity islands of the pre-pandemic and pandemic strains. In addition, the results of single nucleotide polymorphism (SNP) analysis showed that 94% of the SNPs between O3:K6 and O4:K68 pandemic isolates were within a 141 kb region surrounding the O- and K-antigen-encoding gene clusters. The "core" genes of V. parahaemolyticus were also compared to those of V. cholerae and V. vulnificus, in order to delineate differences between these three pathogenic species. Approximately one-half (49-59%) of each species' core genes were conserved in all three species, and 14-24% of the core genes were species-specific and in different functional categories.

CONCLUSIONS

Our data support the idea that the pandemic strains are closely related and that recent South American outbreaks of foodborne disease caused by V. parahaemolyticus are closely linked to outbreaks in India. Serotype conversion from O3:K6 to O4:K68 was likely due to a recombination event involving a region much larger than the O-antigen- and K-antigen-encoding gene clusters. Major differences between pathogenicity islands and mobile elements are also likely driving the evolution of V. parahaemolyticus. In addition, our analyses categorized genes that may be useful in differentiating pathogenic Vibrios at the species level.

Genetic analysis of the capsule polysaccharide (K antigen) and exopolysaccharide genes in pandemic Vibrio parahaemolyticus O3:K6

BACKGROUND

Pandemic Vibrio parahaemolyticus has undergone rapid changes in both K- and O-antigens, making detection of outbreaks more difficult. In order to understand these rapid changes, the genetic regions encoding these antigens must be examined. In Vibrio cholerae and Vibrio vulnificus, both O-antigen and capsular polysaccharides are encoded in a single region on the large chromosome; a similar arrangement in pandemic V. parahaemolyticus would help explain the rapid serotype changes. However, previous reports on "capsule" genes are controversial. Therefore, we set out to clarify and characterize these regions in pandemic V. parahaemolyticus O3:K6 by gene deletion using a chitin based transformation strategy.

RESULTS

We generated different deletion mutants of putative polysaccharide genes and examined the mutants by immuno-blots with O and K specific antisera. Our results showed that O- and K-antigen genes are separated in V. parahaemolyticus O3:K6; the region encoding both O-antigen and capsule biosynthesis in other vibrios, i.e. genes between gmhD and rjg, determines the K6-antigen but not the O3-antigen in V. parahaemolyticus. The previously identified "capsule genes" on the smaller chromosome were related to exopolysaccharide synthesis, not K-antigen.

CONCLUSION

Understanding of the genetic basis of O- and K-antigens is critical to understanding the rapid changes in these polysaccharides seen in pandemic V. parahaemolyticus. This report confirms the genetic location of K-antigen synthesis in V. parahaemolyticus O3:K6 allowing us to focus future studies of the evolution of serotypes to this region.